AMBER Archive (2006)

Subject: Re: AMBER: generate "template" frcmod from standard residues?

From: mernst_at_tricity.wsu.edu
Date: Thu Aug 17 2006 - 12:06:07 CDT

>> I need a frcmod file. But from the manual and mailing list it seems that
>> only parmchk generates frcmod files automatically, and it only generates
>> entries for missing parameters or types. I would like to generate a frcmod
>> file that contains all entries for a residue, not just the missing ones.
>
> This is just a guess: have you tried creating a almost-empty gaff.dat file?
> That is, one that has just one bond, one angle, etc which are not in your
> system. It seems to me that then parmchk would not find any of the needed
> parameters, and would provide a template that included all of them.
>
> ...dac
If I do that, won't the template be devoid of assigned parameters? I want the parameters
to initially reflect the standard force field parameters for a standard nucleotide so
that I can alter them a bit rather than parameterizing the entire residue by hand. Maybe
altered amino acids and nucleotides are less commonly used than I imagined.

Matt Ernst
Washington State University

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